Have you used the site yourself?
I can not really understand what I see.
If I for example search for PDIA2, (Symbols and accessions; species: homo sapiens), I got three diagrams which seems to be the same but look very, very different.

What is it that I see? Someone who knows?
The FAQ are not working. (server can not be found).

The Gene Expression Atlas (GNF) can be a little buggy. It's been a while since I last used it, but here is what I remember.

At the top, there will be a horizontal bar with a "Search" box in it. Enter "PDIA2" and hit Enter. If you have JavaScript active, a navigation box will appear to the left. In the bottom of this box is a "Search Results List" which contains an entry for "Homo sapiens." Click the link for PDIA2 in this list. This will load a data table with a bunch of annotation for this gene. To get its tissue-specific expression data (note: GNF doesn't record actual protein levels, but mRNA levels), go to the left navigation box again and change the "View/Do" setting to "Profiles Only." This pops up three separate images - three sideways bar graphs with tissues on the y-axis and expression levels on the x-axis.

If memory serves, each of these graphs corresponds to a single Affymetrix reporter for the gene. In other words, each of these graphs measures the expression of a single, distinct probe sequence in a gene expression microarray analysis.

To search on gene expression, click the "Search Expression" tab on the upper bar. This tool lets you go in the reverse direction - if you want to find all genes with probes that express highly in, let's say, the human pancreas, you would set the data source to "Human GeneAtlas GNF1H, gcRMA" (you can use MAS5, too, but I prefer gcRMA), then go down to the "Pancreas" field, set the operator to ">," and put "5" in the Fold X box. This should pull up 329 genes. You can use other Fold X as well to increase or decrease the size of your result set.

Clearer? Play around with this tool awhile and if you have specific questions then ask me.

1) What is the difference between the gcRMA and MAS5? I read that MAS5 was an algorithm, does this mean that this is the same data analyzed in different ways?

2) I did not understand your answer: "each of these graphs corresponds to a single Affymetrix reporter for the gene"

This must mean that it is different probes for the same genes. And in this case the results should be about the same. And for PDIA2 it is not. According two one graph it is only almost expressed in pancreas, but not in the others.

gcRMA and MAS5 are normalization techniques for normalizing spot intensities in Affymetrix slides. Most of the reports I've seen that contrast the two say "go with gcRMA."

"And in this case the results should be about the same." No! What about alternative splicing and alternate transcripts? If each reporter comes from a different splice variant, then you can get wildly different profiles for each reporter. You need to figure out what reporter you're interested in (most likely the one that corresponds to the major splice variant) and look at that profile. Unfortunately, I'm not sure how to do that in GNF Atlas, but there must be a way. You'll have to play around with it until you figure it out.